SelfRegulatingGeneSwitch.h

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/*
 * University of Illinois Open Source License
 * Copyright 2010-2018 Luthey-Schulten Group,
 * All rights reserved.
 * 
 * Developed by: Luthey-Schulten Group
 *               University of Illinois at Urbana-Champaign
 *               http://www.scs.uiuc.edu/~schulten
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 * this software and associated documentation files (the Software), to deal with 
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 * use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies 
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 * - Redistributions of source code must retain the above copyright notice, 
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 * Author(s): Elijah Roberts
 */
 
#ifndef LM_CME_SELFREGULATINGGENESWITCH_H_
#define LM_CME_SELFREGULATINGGENESWITCH_H_
 
#include <cmath>
#include <map>
#include <string>
#include "cme/NextReactionSolver.h"
#include "ParameterValues.pb.h"
 
using std::string;
using std::map;
using lm::io::ParameterValues;
 
namespace lm {
namespace cme {
 
class SelfRegulatingGeneSwitch: public NextReactionSolver
{
protected:
    struct OUKHillPropensityArgs
    {
        OUKHillPropensityArgs(uint xi, uint oui, double kmin, double kmax, double x50, double noiseVariance, double noiseTau, RandomGenerator * rng):xi(xi),oui(oui),kmin(kmin),dk(kmax-kmin),x50sq(x50*x50),noiseVariance(noiseVariance),noiseTau(noiseTau),noise(0.0),lastOUJumpNumber(0),previousTime(0.0),rng(rng),rngNext(TUNE_LOCAL_RNG_CACHE_SIZE) {}
        ~OUKHillPropensityArgs() {}
        uint xi;
        uint oui;
        double kmin;
        double dk;
        double x50sq;
        double noiseVariance;
        double noiseTau;
        double noise;
        uint lastOUJumpNumber;
        double previousTime;
        RandomGenerator * rng;
        double normRngValues[TUNE_LOCAL_RNG_CACHE_SIZE];
        int rngNext;
    };
 
public:
    SelfRegulatingGeneSwitch();
    virtual ~SelfRegulatingGeneSwitch();
    virtual bool needsReactionModel() {return false;}
    virtual bool needsDiffusionModel()  {return false;}
    virtual void generateTrajectory();
    
protected:
    static double ouKHillPropensity(double time, uint * speciesCounts, void * pargs);
};
 
}
}
 
#endif